Truth.resample#
missionbio.demultiplex.dna.truth.Truth.resample
- Truth.resample(rule, axis: Axis = 0, closed: str | None = None, label: str | None = None, convention: str = 'start', kind: str | None = None, loffset=None, base: int | None = None, on: Level = None, level: Level = None, origin: str | TimestampConvertibleTypes = 'start_day', offset: TimedeltaConvertibleTypes | None = None, group_keys: bool | lib.NoDefault = _NoDefault.no_default) Resampler#
Resample time-series data.
Convenience method for frequency conversion and resampling of time series. The object must have a datetime-like index (DatetimeIndex, PeriodIndex, or TimedeltaIndex), or the caller must pass the label of a datetime-like series/index to the
on/levelkeyword parameter.- Parameters:
- ruleDateOffset, Timedelta or str
The offset string or object representing target conversion.
- axis{0 or ‘index’, 1 or ‘columns’}, default 0
Which axis to use for up- or down-sampling. For Series this parameter is unused and defaults to 0. Must be DatetimeIndex, TimedeltaIndex or PeriodIndex.
- closed{‘right’, ‘left’}, default None
Which side of bin interval is closed. The default is ‘left’ for all frequency offsets except for ‘M’, ‘A’, ‘Q’, ‘BM’, ‘BA’, ‘BQ’, and ‘W’ which all have a default of ‘right’.
- label{‘right’, ‘left’}, default None
Which bin edge label to label bucket with. The default is ‘left’ for all frequency offsets except for ‘M’, ‘A’, ‘Q’, ‘BM’, ‘BA’, ‘BQ’, and ‘W’ which all have a default of ‘right’.
- convention{‘start’, ‘end’, ‘s’, ‘e’}, default ‘start’
For PeriodIndex only, controls whether to use the start or end of rule.
- kind{‘timestamp’, ‘period’}, optional, default None
Pass ‘timestamp’ to convert the resulting index to a DateTimeIndex or ‘period’ to convert it to a PeriodIndex. By default the input representation is retained.
- loffsettimedelta, default None
Adjust the resampled time labels.
Deprecated since version 1.1.0: You should add the loffset to the df.index after the resample. See below.
- baseint, default 0
For frequencies that evenly subdivide 1 day, the “origin” of the aggregated intervals. For example, for ‘5min’ frequency, base could range from 0 through 4. Defaults to 0.
Deprecated since version 1.1.0: The new arguments that you should use are ‘offset’ or ‘origin’.
- onstr, optional
For a DataFrame, column to use instead of index for resampling. Column must be datetime-like.
- levelstr or int, optional
For a MultiIndex, level (name or number) to use for resampling. level must be datetime-like.
- originTimestamp or str, default ‘start_day’
The timestamp on which to adjust the grouping. The timezone of origin must match the timezone of the index. If string, must be one of the following:
‘epoch’: origin is 1970-01-01
‘start’: origin is the first value of the timeseries
‘start_day’: origin is the first day at midnight of the timeseries
New in version 1.1.0.
‘end’: origin is the last value of the timeseries
‘end_day’: origin is the ceiling midnight of the last day
New in version 1.3.0.
- offsetTimedelta or str, default is None
An offset timedelta added to the origin.
New in version 1.1.0.
- group_keysbool, optional
Whether to include the group keys in the result index when using
.apply()on the resampled object. Not specifyinggroup_keyswill retain values-dependent behavior from pandas 1.4 and earlier (see pandas 1.5.0 Release notes for examples). In a future version of pandas, the behavior will default to the same as specifyinggroup_keys=False.New in version 1.5.0.
- Returns:
- pandas.core.Resampler
Resamplerobject.
See also
Notes
See the user guide for more.
To learn more about the offset strings, please see this link.
Examples
Start by creating a series with 9 one minute timestamps.
>>> index = pd.date_range('1/1/2000', periods=9, freq='T') >>> series = pd.Series(range(9), index=index) >>> series 2000-01-01 00:00:00 0 2000-01-01 00:01:00 1 2000-01-01 00:02:00 2 2000-01-01 00:03:00 3 2000-01-01 00:04:00 4 2000-01-01 00:05:00 5 2000-01-01 00:06:00 6 2000-01-01 00:07:00 7 2000-01-01 00:08:00 8 Freq: T, dtype: int64
Downsample the series into 3 minute bins and sum the values of the timestamps falling into a bin.
>>> series.resample('3T').sum() 2000-01-01 00:00:00 3 2000-01-01 00:03:00 12 2000-01-01 00:06:00 21 Freq: 3T, dtype: int64
Downsample the series into 3 minute bins as above, but label each bin using the right edge instead of the left. Please note that the value in the bucket used as the label is not included in the bucket, which it labels. For example, in the original series the bucket
2000-01-01 00:03:00contains the value 3, but the summed value in the resampled bucket with the label2000-01-01 00:03:00does not include 3 (if it did, the summed value would be 6, not 3). To include this value close the right side of the bin interval as illustrated in the example below this one.>>> series.resample('3T', label='right').sum() 2000-01-01 00:03:00 3 2000-01-01 00:06:00 12 2000-01-01 00:09:00 21 Freq: 3T, dtype: int64
Downsample the series into 3 minute bins as above, but close the right side of the bin interval.
>>> series.resample('3T', label='right', closed='right').sum() 2000-01-01 00:00:00 0 2000-01-01 00:03:00 6 2000-01-01 00:06:00 15 2000-01-01 00:09:00 15 Freq: 3T, dtype: int64
Upsample the series into 30 second bins.
>>> series.resample('30S').asfreq()[0:5] # Select first 5 rows 2000-01-01 00:00:00 0.0 2000-01-01 00:00:30 NaN 2000-01-01 00:01:00 1.0 2000-01-01 00:01:30 NaN 2000-01-01 00:02:00 2.0 Freq: 30S, dtype: float64
Upsample the series into 30 second bins and fill the
NaNvalues using theffillmethod.>>> series.resample('30S').ffill()[0:5] 2000-01-01 00:00:00 0 2000-01-01 00:00:30 0 2000-01-01 00:01:00 1 2000-01-01 00:01:30 1 2000-01-01 00:02:00 2 Freq: 30S, dtype: int64
Upsample the series into 30 second bins and fill the
NaNvalues using thebfillmethod.>>> series.resample('30S').bfill()[0:5] 2000-01-01 00:00:00 0 2000-01-01 00:00:30 1 2000-01-01 00:01:00 1 2000-01-01 00:01:30 2 2000-01-01 00:02:00 2 Freq: 30S, dtype: int64
Pass a custom function via
apply>>> def custom_resampler(arraylike): ... return np.sum(arraylike) + 5 ... >>> series.resample('3T').apply(custom_resampler) 2000-01-01 00:00:00 8 2000-01-01 00:03:00 17 2000-01-01 00:06:00 26 Freq: 3T, dtype: int64
For a Series with a PeriodIndex, the keyword convention can be used to control whether to use the start or end of rule.
Resample a year by quarter using ‘start’ convention. Values are assigned to the first quarter of the period.
>>> s = pd.Series([1, 2], index=pd.period_range('2012-01-01', ... freq='A', ... periods=2)) >>> s 2012 1 2013 2 Freq: A-DEC, dtype: int64 >>> s.resample('Q', convention='start').asfreq() 2012Q1 1.0 2012Q2 NaN 2012Q3 NaN 2012Q4 NaN 2013Q1 2.0 2013Q2 NaN 2013Q3 NaN 2013Q4 NaN Freq: Q-DEC, dtype: float64
Resample quarters by month using ‘end’ convention. Values are assigned to the last month of the period.
>>> q = pd.Series([1, 2, 3, 4], index=pd.period_range('2018-01-01', ... freq='Q', ... periods=4)) >>> q 2018Q1 1 2018Q2 2 2018Q3 3 2018Q4 4 Freq: Q-DEC, dtype: int64 >>> q.resample('M', convention='end').asfreq() 2018-03 1.0 2018-04 NaN 2018-05 NaN 2018-06 2.0 2018-07 NaN 2018-08 NaN 2018-09 3.0 2018-10 NaN 2018-11 NaN 2018-12 4.0 Freq: M, dtype: float64
For DataFrame objects, the keyword on can be used to specify the column instead of the index for resampling.
>>> d = {'price': [10, 11, 9, 13, 14, 18, 17, 19], ... 'volume': [50, 60, 40, 100, 50, 100, 40, 50]} >>> df = pd.DataFrame(d) >>> df['week_starting'] = pd.date_range('01/01/2018', ... periods=8, ... freq='W') >>> df price volume week_starting 0 10 50 2018-01-07 1 11 60 2018-01-14 2 9 40 2018-01-21 3 13 100 2018-01-28 4 14 50 2018-02-04 5 18 100 2018-02-11 6 17 40 2018-02-18 7 19 50 2018-02-25 >>> df.resample('M', on='week_starting').mean() price volume week_starting 2018-01-31 10.75 62.5 2018-02-28 17.00 60.0
For a DataFrame with MultiIndex, the keyword level can be used to specify on which level the resampling needs to take place.
>>> days = pd.date_range('1/1/2000', periods=4, freq='D') >>> d2 = {'price': [10, 11, 9, 13, 14, 18, 17, 19], ... 'volume': [50, 60, 40, 100, 50, 100, 40, 50]} >>> df2 = pd.DataFrame( ... d2, ... index=pd.MultiIndex.from_product( ... [days, ['morning', 'afternoon']] ... ) ... ) >>> df2 price volume 2000-01-01 morning 10 50 afternoon 11 60 2000-01-02 morning 9 40 afternoon 13 100 2000-01-03 morning 14 50 afternoon 18 100 2000-01-04 morning 17 40 afternoon 19 50 >>> df2.resample('D', level=0).sum() price volume 2000-01-01 21 110 2000-01-02 22 140 2000-01-03 32 150 2000-01-04 36 90
If you want to adjust the start of the bins based on a fixed timestamp:
>>> start, end = '2000-10-01 23:30:00', '2000-10-02 00:30:00' >>> rng = pd.date_range(start, end, freq='7min') >>> ts = pd.Series(np.arange(len(rng)) * 3, index=rng) >>> ts 2000-10-01 23:30:00 0 2000-10-01 23:37:00 3 2000-10-01 23:44:00 6 2000-10-01 23:51:00 9 2000-10-01 23:58:00 12 2000-10-02 00:05:00 15 2000-10-02 00:12:00 18 2000-10-02 00:19:00 21 2000-10-02 00:26:00 24 Freq: 7T, dtype: int64
>>> ts.resample('17min').sum() 2000-10-01 23:14:00 0 2000-10-01 23:31:00 9 2000-10-01 23:48:00 21 2000-10-02 00:05:00 54 2000-10-02 00:22:00 24 Freq: 17T, dtype: int64
>>> ts.resample('17min', origin='epoch').sum() 2000-10-01 23:18:00 0 2000-10-01 23:35:00 18 2000-10-01 23:52:00 27 2000-10-02 00:09:00 39 2000-10-02 00:26:00 24 Freq: 17T, dtype: int64
>>> ts.resample('17min', origin='2000-01-01').sum() 2000-10-01 23:24:00 3 2000-10-01 23:41:00 15 2000-10-01 23:58:00 45 2000-10-02 00:15:00 45 Freq: 17T, dtype: int64
If you want to adjust the start of the bins with an offset Timedelta, the two following lines are equivalent:
>>> ts.resample('17min', origin='start').sum() 2000-10-01 23:30:00 9 2000-10-01 23:47:00 21 2000-10-02 00:04:00 54 2000-10-02 00:21:00 24 Freq: 17T, dtype: int64
>>> ts.resample('17min', offset='23h30min').sum() 2000-10-01 23:30:00 9 2000-10-01 23:47:00 21 2000-10-02 00:04:00 54 2000-10-02 00:21:00 24 Freq: 17T, dtype: int64
If you want to take the largest Timestamp as the end of the bins:
>>> ts.resample('17min', origin='end').sum() 2000-10-01 23:35:00 0 2000-10-01 23:52:00 18 2000-10-02 00:09:00 27 2000-10-02 00:26:00 63 Freq: 17T, dtype: int64
In contrast with the start_day, you can use end_day to take the ceiling midnight of the largest Timestamp as the end of the bins and drop the bins not containing data:
>>> ts.resample('17min', origin='end_day').sum() 2000-10-01 23:38:00 3 2000-10-01 23:55:00 15 2000-10-02 00:12:00 45 2000-10-02 00:29:00 45 Freq: 17T, dtype: int64
To replace the use of the deprecated base argument, you can now use offset, in this example it is equivalent to have base=2:
>>> ts.resample('17min', offset='2min').sum() 2000-10-01 23:16:00 0 2000-10-01 23:33:00 9 2000-10-01 23:50:00 36 2000-10-02 00:07:00 39 2000-10-02 00:24:00 24 Freq: 17T, dtype: int64
To replace the use of the deprecated loffset argument:
>>> from pandas.tseries.frequencies import to_offset >>> loffset = '19min' >>> ts_out = ts.resample('17min').sum() >>> ts_out.index = ts_out.index + to_offset(loffset) >>> ts_out 2000-10-01 23:33:00 0 2000-10-01 23:50:00 9 2000-10-02 00:07:00 21 2000-10-02 00:24:00 54 2000-10-02 00:41:00 24 Freq: 17T, dtype: int64
< Class Truth